1. Volume 26, Issue 3, Pages 344-350 (February 2016)
Divergence and Functional Degradation of a Sex Chromosome-like Supergene 
Elaina M. Tuttle, Alan O. Bergland, Marisa L. Korody, Michael S. Brewer, Daniel J. Newhouse, Patrick Minx, Maria Stager, Adam Betuel, Zachary A. Cheviron, Wesley C. Warren, Rusty A. Gonser, Christopher N. Balakrishnan 
Current Biology 
Volume 26, Issue 3, Pages (February 2016)
DOI: /j.cub
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2. Current Biology 2016 26, 344-350DOI: (10.1016/j.cub.2015.11.069)
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3. Figure 1
White-Throated Sparrows Comprise Two Morphs with an Ancient Origin
(A) Tan (T) and white (W) morph sparrows (note differences in plumage color in the head stripe and throat) differ in chromosome 2 (sometimes referred to as ZAL2) genotype and mate almost exclusively with the opposite morph, maintaining polymorphism in the species.
(B) Tan (2) and white (2m) chromosomes are highly divergent within the inverted portion of the chromosome, suggesting an ancient origin of the chromosomes 2 and 2m. All nodes are supported by 100% bootstrap values, and the depicted topology for the inverted region is a significantly better fit to the data than trees constrained to the monophyly of 2 and 2m (p < 0.001; see the Supplemental Experimental Procedures). Taxa marked with an asterisk are those for which whole genomes were sequenced. The arrows highlight the ancestral node for the Zonotrichia genus.
See also Table S2.
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4. Figure 2 Contrasting Divergence, Diversity, and Linkage Disequilibrium
(A and B) Sliding window estimate across FISH-mapped scaffolds of (A) FST between white and tan birds and (B) genetic diversity along the tan allele, 2. The gray bars represent the 95% confidence band (SD). The pink area indicates the region inside the inversion, whereas the uncolored area represents the area outside the inversion.
(C) Linkage disequilibrium decays rapidly outside of the inversion, but is high, especially in 2/2m heterozygotes, within the inversion.
(D) Using golden-crowned (GC) or Harris’s sparrows as outgroups, Fay and Wu’s H estimates [26] do not show a strong signal of recent selective sweeps in the inverted region of chromosome 2.
See also Figures S1 and S3 and Table S3.
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5. Figure 3 Functional Degradation of 2m
(A) Using two different outgroups (diamond, golden-crowned sparrow; circle, Harris’ sparrow), the direction of selection statistic is strongly negative on 2m, indicating an increased level of non-synonymous polymorphism. When the DoS is calculated between 2 and 2m (Inv. 2/2m), the signature is similar to the neutral expectation, suggesting that the two alleles came together only recently.
(B) For genes within the inversion, gene expression is higher for tan birds than heterozygous (2/2m) white-morph birds.
(C) In white birds, the white (2m) allele tends to be underexpressed relative to the tan (2) allele.
∗∗p < 0.01; ∗∗∗p < Error bars represent 95% confidence intervals (SE). See also Figures S2 and S4 and Table S1.
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